Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

Abstract

BackgroundNext-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities.ResultsMitochondrial enrichment directly followed by Illumina shotgun sequencing, at an ultra-high sequence volume, enabled the recovery of Cytochrome c Oxidase subunit 1 (COI) barcode sequences, which allowed for the estimation of species composition at high fidelity for a terrestrial insect community. With 15.5 Gbp Illumina data, approximately 97% and 92% were detected out of the 37 input Operational Taxonomic Units (OTUs), whether the reference barcode library was used or not, respectively, while only 1 novel OTU was found for the latter. Additionally, relatively strong correlation between the sequencing volume and the total biomass was observed for species from the bulk sample, suggesting a potential solution to reveal relative abundance.ConclusionsThe ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs. However, further improvement for mitochondrial enrichment is likely needed for the application of the new pipeline in analyzing arthropod communities at higher diversity.

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

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Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

“…Enrichment of targeted molecules such as mitochondrial DNA may improve the problems associated with insufficient sequencing depth (Zhou et al 2013). Nonetheless, vast amounts of functional data produced in the metagenomics analyses promise a new paradigm in community ecology (Zhou et al 2015).…”

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DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

“…This finding is noteworthy because many ecological assessments work at the level of functional groups rather than at the level of species. Alternatively, PCR-free shotgun metagenomic approaches will be less prone to bias but require much higher sequencing depth (15), therefore increasing the cost for sufficient replication. Taxonomic coverage among animals will also increase with sequencing multiple independent markers [i.e., 18S, 16S (16)], but targeting nonprotein-coding genes may increase the probability of including sequencing artifacts.…”